Michael Stadler
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/QuasR |
| Branch: RELEASE_3_9 |
| Last Commit: cd8a370 |
| Last Changed Date: 2019-05-17 04:18:23 -0400 (Fri, 17 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:27:23 -0400 (Wed, 16 Oct 2019).
| Package 1296/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| QuasR 1.24.2 Michael Stadler
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | [ OK ] | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: QuasR |
| Version: 1.24.2 |
| Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch --build --library=QuasR.buildbin-libdir QuasR_1.24.2.tar.gz |
| StartedAt: 2019-10-16 09:59:28 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 10:01:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 102.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: QuasR_1.24.2.zip |
| PackageFileSize: 2.598 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch --build --library=QuasR.buildbin-libdir QuasR_1.24.2.tar.gz
###
##############################################################################
##############################################################################
* installing *source* package 'QuasR' ...
** using staged installation
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_init_QuasR.cpp -o R_init_QuasR.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c bam.c -o bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c bam_cat.c -o bam_cat.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c cat_bam.c -o cat_bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c count_alignments.c -o count_alignments.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c count_alignments_subregions.c -o count_alignments_subregions.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c count_junctions.cpp -o count_junctions.o
count_junctions.cpp: In function 'int _addJunction(const bam1_t*, void*)':
count_junctions.cpp:90:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = y = 0; i < hit->core.n_cigar; ++i) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c export_wig.c -o export_wig.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extract_unmapped_reads.c -o extract_unmapped_reads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c filter_hisat2.c -o filter_hisat2.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c idxstats_bam.c -o idxstats_bam.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c merge_reorder_sam.cpp -o merge_reorder_sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c profile_alignments.c -o profile_alignments.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c quantify_methylation.cpp -o quantify_methylation.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sam_utils.c -o sam_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c split_sam_chr.c -o split_sam_chr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o bam.o bam_cat.o bam_plbuf.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o filter_hisat2.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o sam.o sam_utils.o split_sam_chr.o utilities.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.9-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/QuasR.buildbin-libdir/00LOCK-QuasR/00new/QuasR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'QuasR'
finding HTML links ... done
QuasR-package html
alignmentStats html
preprocessReads html
qAlign html
qCount html
qExportWig html
qMeth html
qProfile html
qProject-class html
qProjectUpdate html
qQCReport html
finding level-2 HTML links ... done
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'QuasR' as QuasR_1.24.2.zip
* DONE (QuasR)